Package: sesame
Type: Package
Title: SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Description: Tools For analyzing Illumina Infinium DNA methylation arrays.SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features more accurate detection calling, intelligenet inference of ethnicity, sex and advanced quality control routines.
Version: 1.12.1
Authors@R: c(person("Wanding", "Zhou", role = c("aut","cre"),
             email = "zhouwanding@gmail.com"),
             person("Hui", "Shen", role = c("aut"),
             email = "Hui.Shen@vai.org"),
             person("Timothy", "Triche", role = "ctb"),
             person("Bret", "Barnes", role = "ctb"))
Depends: R (>= 4.1), sesameData, methods
License: MIT + file LICENSE
RoxygenNote: 7.1.2
Imports: BiocParallel, grDevices, utils, stringr, tibble, illuminaio,
        MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors,
        randomForest, wheatmap, ggplot2, graphics, KernSmooth,
        parallel, matrixStats, DNAcopy, stats, SummarizedExperiment,
        e1071, fgsea, ggrepel, reshape2
Suggests: scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle,
        IlluminaHumanMethylation450kmanifest, minfi,
        FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k,
        HDF5Array
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/zwdzwd/sesame
BugReports: https://github.com/zwdzwd/sesame/issues
biocViews: DNAMethylation, MethylationArray, Preprocessing,
        QualityControl
Collate: 'sex.R' 'species.R' 'QC.R' 'GEO.R' 'SigDFMethods.R' 'sesame.R'
        'age.R' 'background_correction.R' 'cell_composition.R'
        'channel_inference.R' 'cnv.R' 'ethnicity.R' 'deidentify.R'
        'detection.R' 'dm.R' 'dye_bias.R' 'feature_selection.R'
        'fileSet.R' 'mask.R' 'open.R' 'sesamize.R' 'snp.R' 'strain.R'
        'tissue.R' 'track.R' 'utils.R' 'vcf.R' 'visualize.R' 'zzz.R'
        'kyCG.R'
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_14
git_last_commit: 671d468
git_last_commit_date: 2021-11-09
Date/Publication: 2021-11-09
NeedsCompilation: no
Packaged: 2021-11-10 06:26:48 UTC; biocbuild
Author: Wanding Zhou [aut, cre],
  Hui Shen [aut],
  Timothy Triche [ctb],
  Bret Barnes [ctb]
Maintainer: Wanding Zhou <zhouwanding@gmail.com>
Built: R 4.1.2; ; 2021-11-10 19:33:24 UTC; unix
